{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:14:07Z","timestamp":1753884847803,"version":"3.41.2"},"reference-count":36,"publisher":"World Scientific Pub Co Pte Ltd","issue":"04","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2024,8]]},"abstract":"<jats:p> Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED\u2019s superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http:\/\/195.251.108.230\/apps.compgen.org\/CW-PRED\/ and as standalone software. <\/jats:p>","DOI":"10.1142\/s0219720024500215","type":"journal-article","created":{"date-parts":[[2024,7,27]],"date-time":"2024-07-27T04:29:41Z","timestamp":1722054581000},"source":"Crossref","is-referenced-by-count":0,"title":["CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea"],"prefix":"10.1142","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-3458-3265","authenticated-orcid":false,"given":"Aikaterini G.","family":"Chatziargyri","sequence":"first","affiliation":[{"name":"Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens Athens 15701, Greece"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-3386-5900","authenticated-orcid":false,"given":"Evangelia 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